Atomistry » Zinc » PDB 3nii-3nn7 » 3nko
Atomistry »
  Zinc »
    PDB 3nii-3nn7 »
      3nko »

Zinc in PDB 3nko: Crystal Structure of Mouse Autotaxin in Complex with 16:0-Lpa

Enzymatic activity of Crystal Structure of Mouse Autotaxin in Complex with 16:0-Lpa

All present enzymatic activity of Crystal Structure of Mouse Autotaxin in Complex with 16:0-Lpa:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Mouse Autotaxin in Complex with 16:0-Lpa, PDB code: 3nko was solved by H.Nishimasu, R.Ishitani, E.Mihara, J.Takagi, J.Aoki, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.45 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.545, 94.403, 75.243, 90.00, 94.98, 90.00
R / Rfree (%) 18.4 / 22.4

Other elements in 3nko:

The structure of Crystal Structure of Mouse Autotaxin in Complex with 16:0-Lpa also contains other interesting chemical elements:

Potassium (K) 1 atom
Calcium (Ca) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mouse Autotaxin in Complex with 16:0-Lpa (pdb code 3nko). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Mouse Autotaxin in Complex with 16:0-Lpa, PDB code: 3nko:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3nko

Go back to Zinc Binding Sites List in 3nko
Zinc binding site 1 out of 2 in the Crystal Structure of Mouse Autotaxin in Complex with 16:0-Lpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Mouse Autotaxin in Complex with 16:0-Lpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:20.5
occ:1.00
OD1 A:ASP171 1.9 16.4 1.0
OG1 A:THR209 2.0 18.1 1.0
NE2 A:HIS359 2.1 14.4 1.0
OD2 A:ASP358 2.1 18.2 1.0
CG A:ASP171 2.6 19.1 1.0
OD2 A:ASP171 2.7 19.7 1.0
CD2 A:HIS359 3.0 15.0 1.0
CG A:ASP358 3.0 18.5 1.0
CE1 A:HIS359 3.0 16.0 1.0
CB A:THR209 3.1 18.4 1.0
OD1 A:ASP358 3.2 16.6 1.0
CG2 A:THR209 3.5 20.2 1.0
CA A:THR209 3.5 16.5 1.0
OAD A:NKO1006 3.7 33.3 1.0
N A:THR209 3.9 16.1 1.0
CB A:ASP171 4.0 18.8 1.0
OAA A:NKO1006 4.0 19.3 1.0
CG A:HIS359 4.1 14.1 1.0
ND1 A:HIS359 4.1 13.0 1.0
OD1 A:ASP311 4.1 17.3 1.0
N A:GLY172 4.1 15.5 1.0
CA A:ASP171 4.3 15.2 1.0
CG A:ASP311 4.3 17.7 1.0
CB A:ASP358 4.4 16.2 1.0
CE1 A:HIS474 4.4 16.3 1.0
PAC A:NKO1006 4.4 28.2 1.0
C A:ASP171 4.5 16.5 1.0
ZN A:ZN1002 4.6 18.1 1.0
CAG A:NKO1006 4.6 32.9 1.0
C A:LYS208 4.6 15.9 1.0
OD2 A:ASP311 4.7 23.7 1.0
NE2 A:HIS474 4.7 17.4 1.0
CB A:ASP311 4.8 19.6 1.0
C A:THR209 4.8 16.3 1.0
CA A:GLY172 4.9 16.2 1.0

Zinc binding site 2 out of 2 in 3nko

Go back to Zinc Binding Sites List in 3nko
Zinc binding site 2 out of 2 in the Crystal Structure of Mouse Autotaxin in Complex with 16:0-Lpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Mouse Autotaxin in Complex with 16:0-Lpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:18.1
occ:1.00
OAD A:NKO1006 1.8 33.3 1.0
NE2 A:HIS315 2.0 18.4 1.0
NE2 A:HIS474 2.0 17.4 1.0
OD1 A:ASP311 2.2 17.3 1.0
OD2 A:ASP311 2.4 23.7 1.0
CG A:ASP311 2.6 17.7 1.0
CE1 A:HIS315 3.0 20.5 1.0
CE1 A:HIS474 3.0 16.3 1.0
CD2 A:HIS315 3.0 18.3 1.0
PAC A:NKO1006 3.0 28.2 1.0
CD2 A:HIS474 3.1 15.6 1.0
OAB A:NKO1006 3.4 36.7 1.0
OAA A:NKO1006 4.0 19.3 1.0
OAF A:NKO1006 4.1 35.1 1.0
CE1 A:HIS359 4.1 16.0 1.0
ND1 A:HIS315 4.1 18.2 1.0
ND1 A:HIS474 4.1 16.4 1.0
CB A:ASP311 4.1 19.6 1.0
CG A:HIS315 4.2 21.3 1.0
CG A:HIS474 4.2 15.0 1.0
NE2 A:HIS359 4.4 14.4 1.0
CE A:MET361 4.4 17.6 1.0
CAG A:NKO1006 4.5 32.9 1.0
OD1 A:ASP171 4.5 16.4 1.0
O A:HOH1079 4.6 32.0 1.0
ZN A:ZN1001 4.6 20.5 1.0
OBA A:NKO1006 4.6 50.5 1.0
OG1 A:THR209 4.7 18.1 1.0
O A:ASP311 4.8 21.2 1.0
CA A:ASP311 4.9 20.5 1.0

Reference:

H.Nishimasu, S.Okudaira, K.Hama, E.Mihara, N.Dohmae, A.Inoue, R.Ishitani, J.Takagi, J.Aoki, O.Nureki. Crystal Structure of Autotaxin and Insight Into Gpcr Activation By Lipid Mediators Nat.Struct.Mol.Biol. V. 18 205 2011.
ISSN: ISSN 1545-9993
PubMed: 21240269
DOI: 10.1038/NSMB.1998
Page generated: Wed Dec 16 04:38:31 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy